Tracing production instability in a clonally derived CHO cell line using single-cell transcriptomics

Area of Science:

• Biotechnology
• Cell Biology
• Molecular Biology

Background:

• Monoclonal antibody (mAb) production in Chinese hamster ovary (CHO) cell lines can be lost through mechanisms like transcriptional silencing or gene copy loss.
• Production instability in CHO cell lines leads to reduced mAb levels, impacting biopharmaceutical manufacturing.

Purpose of the Study:

• To investigate the molecular mechanisms behind mAb production instability in a clonally derived CHO cell line using single-cell RNA sequencing (scRNA-seq).
• To identify cell subclusters and gene expression changes associated with reduced mAb production.

Main Methods:

• Utilized scRNA-seq to analyze a CHO cell line exhibiting production instability.
• Applied trajectory inference to reconstruct cell line evolution and correlate gene expression changes.
• Analyzed gene expression patterns related to mAb transgenes, oxidative stress, and apoptosis.

Main Results:

• Identified subclusters within the CHO cell line associated with variations in mAb transgenes.
• Observed significantly lower heavy chain gene expression compared to light chain expression across the cell population.
• Demonstrated a correlation between cell line evolution, reduced heavy and light chain gene expression, and increased expression of genes involved in oxidative stress and apoptosis.

Conclusions:

• scRNA-seq is a powerful tool for understanding CHO cell line production instability.
• Reduced mAb heavy and light chain expression, coupled with stress responses, contributes to production loss.
• Further research using scRNA-seq can enhance understanding of CHO cell manufacturing performance and product quality.